October 14, 2012

Genes are expressed at widely differing levels

  • The abundance of an mRNA is the average number of molecules per cell.
  • Abundant mRNAs consist of a small number of individual species, each present in a large number of copies per cell.
  • Scarce mRNA (Complex mRNA) consists of a large number of individual mRNA species, each present in very few copies per cell. This accounts for most of the sequence complexity in RNA.
  • In any given cell, most genes are expressed at a low level.
  • Only a small number of genes, whose products are specialized for the cell type, are highly expressed. 

The proportion of DNA represented in an mRNA population can be determined by the amount of the DNA that can hybridize with the RNA. Such a saturation analysis typically identifies ~1% of the DNA as providing a template for mRNA. From this we can calculate the number of genes so long as we know the average length of an mRNA. For a lower eukaryote such as yeast, the total number of expressed genes is ~4000. For somatic tissues of higher eukaryotes, the number usually is 10,000-15,000. The value is similar for plants and for vertebrates. (The only consistent exception to this type of value is presented by mammalian brain, where much larger numbers of genes appear to be expressed, although the exact quantitation is not certain.)
Kinetic analysis of the reassociation of an RNA population can be used to determine its sequence complexity (see 32.1 DNA reassociation kinetics). This type of analysis typically identifies three components in a eukaryotic cell. Just as with a DNA reassociation curve, a single component hybridizes over about two decades of Rot (RNA concentration × time) values, and a reaction extending over a greater range must be resolved by computer curve-fitting into individual components. Again this represents what is really a continuous spectrum of sequences.

An example of an excess mRNA × cDNA reaction that generates three components is given in Figure 3.33:
  • The first component has the same characteristics as a control reaction of ovalbumin mRNA with its DNA copy. This suggests that the first component is in fact just ovalbumin mRNA (which indeed occupies about half of the messenger mass in oviduct tissue).
  • The next component provides 15% of the reaction, with a total complexity of 15 kb. This corresponds to 7-8 mRNA species of average length 2000 bases.
  • The last component provides 35% of the reaction, which corresponds to a complexity of 26 Mb. This corresponds to ~13,000 mRNA species of average length 2000 bases.
From this analysis, we can see that about half of the mass of mRNA in the cell represents a single mRNA, ~15% of the mass is provided by a mere 7-8 mRNAs, and ~35% of the mass is divided into the large number of 13,000 mRNA species. It is therefore obvious that the mRNAs comprising each component must be present in very different amounts.
The average number of molecules of each mRNA per cell is called its abundance. It can be calculated quite simply if the total mass of RNA in the cell is known. In the example shown in Figure 3.33, the total mRNA can be accounted for as 100,000 copies of the first component (ovalbumin mRNA), 4000 copies of each of the 7-8 mRNAs in the second component, but only ~5 copies of each of the 13,000 mRNAs that constitute the last component.
We can divide the mRNA population into two general classes, according to their abundance:
  • The oviduct is an extreme case, with so much of the mRNA represented in only one species, but most cells do contain a small number of RNAs present in many copies each. This abundant mRNA component typically consists of <100 different mRNAs present in 1000-10,000 copies per cell. It often corresponds to a major part of the mass, approaching 50% of the total mRNA.
  • About half of the mass of the mRNA consists of a large number of sequences, of the order of 10,000, each represented by only a small number of copies in the mRNAsay, <10. This is the scarce mRNA or complex mRNA class. It is this class that drives a saturation reaction (Hastie and Bishop, 1976). 

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